AMBER Archive (2003)

Subject: AMBER: MeCNBOX

From: northrop_at_chem.ucla.edu
Date: Thu Sep 25 2003 - 14:35:03 CDT

Amber users - I'd like to run some simulations in an acetonitrile solvent but I don't know how to
make a pre-equilibrated solvent box similar to those that exist for CHCl3, water, etc. The
parameters I'm using for acetonitrile are those from the six-site model of Jaime et. al. (JOC,
 21, 10, 901- 908). My procedure for trying to equilibrate a box of acetonitriile is as follows:
in leap, I set the restype of MeCN to solvent and then solvate a 10 Å box on MeCN
1000 step steepest descent minimization
20 ps constant volume run to raise the temp to 300 k
200 ps constant pressure run to equilibrate
Unfortunately the program always fails with the error message "EWALD BOMB in subroutine,
ewald_list, volume of ucell too big, too many subcells, list grid memory needs to be reallocated,
restart sander." When I look at the restart file, there are large voids of no solvent within the
periodic boundary. Any help anyone could give me about how to make a pre-equilibrated
MeCNBOX would be greatly appreciated.

thanks in advance,
Brian Northrop

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